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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod373

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod373 Module size 3 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 4495 MT1G metallothionein 1G 4496 MT1H metallothionein 1H 84651 SPINK7 serine peptidase inhibitor, Kazal type 7 (putative)

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 1.79e-02 3.73e-07 Reactome Metallothioneins bind metals Cellular responses to external stimuli

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 2.96e-05 1.02e-02 cellular response to zinc ion 2.99e-05 1.02e-02 cellular response to cadmium ion 6.04e-05 1.89e-02 response to cadmium ion 8.08e-05 2.43e-02 cellular response to metal ion 8.12e-05 2.44e-02 cellular response to inorganic substance 1.83e-04 4.86e-02 negative regulation of growth 2.07e-04 5.39e-02 response to zinc ion 5.09e-04 1.14e-01 response to metal ion 9.36e-04 1.87e-01 response to inorganic substance 1.50e-03 2.75e-01 regulation of growth 1.95e-03 3.34e-01 response to copper ion 1.95e-03 3.34e-01 cellular response to copper ion 1.95e-03 3.34e-01 monocyte activation 1.95e-03 3.34e-01 cellular response to vascular endothelial growth factor stimulus 1.95e-03 3.34e-01 monocyte differentiation 5.86e-03 7.72e-01 myeloid leukocyte differentiation 7.48e-03 7.52e-01 perinuclear region of cytoplasm 9.69e-03 1.00e+00 negative regulation of serine-type endopeptidase activity 9.70e-03 1.00e+00 regulation of acrosome reaction 1.01e-02 9.36e-01 acrosomal vesicle

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)